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The availability of chemical energy supplies is fundamental to environmental and planetary habitability. However, the presence of a chemical energy supply does not guarantee the presence of microorganisms capable of consuming it. In this study, chemical energy supplies available in Yellowstone National Park (YNP) hot springs were calculated, and the results indicate that ammonia oxidation, calculated using total dissolved ammonia, is one of the major energy supplies. Nevertheless, known ammonia-oxidizers (AO) are only present in a small fraction of the hot springs tested. Where AO are present, they do not dominate the microbial communities (relative abundances <5%), even in cases where total dissolved ammonia oxidation is the richest energy supply. The AO in YNP hot springs are predominantly ammonia-oxidizing archaea (AOA), which tend to favor environments with low total ammonia (sum of NH3 and NH4+) concentrations, despite the requirement of ammonia (NH3) as a substrate. Hot spring pH and temperature determine the ratio of NH3 to NH4+ and, consequently, NH3 availability to resident AOA. In this study, total ammonia measurements were collected from YNP hot spring samples using ion chromatography in coordination with biological sampling. DNA was extracted from simultaneously collected samples for 16S rRNA gene sequencing and analysis, and for the identification of known AOA. The WORM-portal (https://worm-portal.asu.edu/) was used to speciate the total ammonia measurements into ammonia and ammonium activities. By performing speciation calculations, we identified a potential lower limit for substrate (NH3) availability and a potential upper limit for NH4+ concentrations for the YNP hot spring AOA. Thus, the niche for AOA across YNP hot springs is dictated by the form of the total dissolved ammonia present, not by the energy supply available for total dissolved ammonia oxidation. 

Large volumes of fluid flow through aged oceanic crust. Given the scale of this water flux, the exchange of organic and inorganic carbon that it mediates between the crust and deep ocean can be significant. However, off-axis carbon fluxes in older oceanic crust are still poorly constrained because access to low-temperature fluids from this environment is limited. At North Pond, a sedimented depression located on 8-million-year-old crust on the flank of the Mid-Atlantic Ridge, circulating crustal fluids are accessible through drilled borehole observatories. Here, fluids are cool (≤ 20°C), oxygenated and bear strong geochemical similarities to bottom seawater. In this study, we report concentrations and isotopic composition of dissolved organic and inorganic carbon from crustal fluids that were sampled six years after the installation of borehole observatories, which better represent the fluid geochemistry prior to drilling and perturbation. Radiocarbon-based signatures within carbon reservoirs support divergent shallow and deep fluid pathways within the crust. We also report a net loss of both dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) from the fluid during isolation in the crust. The removal of DOC is isotopically selective and consistent with microbe-mediated DOC oxidation. The loss of DIC is consistent with carbonate precipitation, although geochemical signatures of DIC addition to the fluids from DOC oxidation and basalt weathering are also evident. Extrapolated to global fluxes, systems like North Pond could be responsible for a net loss of ~10^11 mol C/yr of DIC and ~10^11 mol C/yr of DOC during the circulation of fluids through oceanic crust at low temperatures. 

ABSTRACT Six marine bacterial isolates were obtained from fluid and sediments collected at alkaline serpentinite mud volcanoes of the Mariana forearc to examine life at high pH in a marine environment. Here, we present the draft genome sequences of these six isolates, classified as strains of the speciesMarinobacter shengliensis. 

Abstract BackgroundMarine symbioses are predominantly established through horizontal acquisition of microbial symbionts from the environment. However, genetic and functional comparisons of free-living populations of symbionts to their host-associated counterparts are sparse. Here, we assembled the first genomes of the chemoautotrophic gammaproteobacterial symbionts affiliated with the deep-sea snailAlviniconcha hesslerifrom two separate hydrothermal vent fields of the Mariana Back-Arc Basin. We used phylogenomic and population genomic methods to assess sequence and gene content variation between free-living and host-associated symbionts. ResultsOur phylogenomic analyses show that the free-living and host-associated symbionts ofA. hesslerifrom both vent fields are populations of monophyletic strains from a single species. Furthermore, genetic structure and gene content analyses indicate that these symbiont populations are differentiated by vent field rather than by lifestyle. ConclusionTogether, this work suggests that, despite the potential influence of host-mediated acquisition and release processes on horizontally transmitted symbionts, geographic isolation and/or adaptation to local habitat conditions are important determinants of symbiont population structure and intra-host composition. 

Biogeochemical processes occurring in fluids that permeate oceanic crust make measurable contributions to the marine carbon cycle, but quantitative assessments of microbial impacts on this vast, subsurface carbon pool are lacking. We provide bulk and single-cell estimates of microbial biomass production from carbon and nitrogen substrates in cool, oxic basement fluids from the western flank of the Mid-Atlantic Ridge. The wide range in carbon and nitrogen incorporation rates indicates a microbial community well poised for dynamic conditions, potentially anabolizing carbon and nitrogen at rates ranging from those observed in subsurface sediments to those found in on-axis hydrothermal vent environments. Bicarbonate incorporation rates were highest where fluids are most isolated from recharging bottom seawater, suggesting that anabolism of inorganic carbon may be a potential strategy for supplementing the ancient and recalcitrant dissolved organic carbon that is prevalent in the globally distributed subseafloor crustal environment. 

Abstract The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust. 

Abstract First reported in the 1960s, offshore freshened groundwater (OFG) has now been documented in most continental margins around the world. In this review we compile a database documenting OFG occurrences and analyze it to establish the general characteristics and controlling factors. We also assess methods used to map and characterize OFG, identify major knowledge gaps, and propose strategies to address them. OFG has a global volume of 1 × 10⁶ km³; it predominantly occurs within 55 km of the coast and down to a water depth of 100 m. OFG is mainly hosted within siliciclastic aquifers on passive margins and recharged by meteoric water during Pleistocene sea level lowstands. Key factors influencing OFG distribution are topography‐driven flow, salinization via haline convection, permeability contrasts, and the continuity/connectivity of permeable and confining strata. Geochemical and stable isotope measurements of pore waters from boreholes have provided insights into OFG emplacement mechanisms, while recent advances in seismic reflection profiling, electromagnetic surveying, and numerical models have improved our understanding of OFG geometry and controls. Key knowledge gaps, such as the extent and function of OFG, and the timing of their emplacement, can be addressed by the application of isotopic age tracers, joint inversion of electromagnetic and seismic reflection data, and development of three‐dimensional hydrological models. We show that such advances, combined with site‐specific modeling, are necessary to assess the potential use of OFG as an unconventional source of water and its role in sub‐seafloor geomicrobiology.